Re: [Gmod-ajax] [apollo] Issues with data visualisation on Apollo

[smm <sm...@eb...>]

Hello,

These are three example commands that I have run. None of them show any 
error. But the visualization is not ideal on Apollo.

1. GFF
~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --gff 
GRCh38_latest_genomic.gff --trackLabel RefSeq_GRCh38 --out dest_loc

2. BigBED to BED
./bigBedToBed mane.0.9.bb mane.0.9.bed
~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --bed 
mane.0.9.bed --trackLabel UCSC_MANE --out dest_loc

3. SQL
~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in 
source_loc --track gtexGene --out dest_loc

Please let me know if you require any other information. The source for 
each file is available here- 
https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing

Regards,
Shamika

On 16/11/2020 16:41, Nathan Dunn wrote:
>
> I’d have to see the individual data and commands you were using for each.
>
> More info can be found here 
> https://jbrowse.org/docs/html_features.html and here 
> https://jbrowse.org/docs/flatfile-to-json.pl.html
>
> That being said, it LOOKS like the filter you are running is for 
> genes, where typically the top-level should be mRNA (for your working 
> attachment), but that is just a guess.
>
> If you provide a snippet, command, and output I can provide some more 
> direct feedback.
>
> Nathan
>
>
>
>> On Nov 16, 2020, at 7:26 AM, Shamika Mohanan <sm...@eb... 
>> <mailto:sm...@eb...>> wrote:
>>
>> Hello,
>>
>> I am trying to load GFF/GTF/BED/BigBED/BAM/UCSC SQL files using the 
>> command line scripts available in Apollo-2.6.1/bin.
>>
>> Most files load properly and are available on Apollo as seen in 
>> attachment_1. There are few files that do load but do not display the 
>> data properly as seen in attachment_2.
>>
>> I have listed the files that show this problem here- 
>> https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing
>>
>> Should I set some option when running the scripts?
>>
>> Regards,
>> Shamika
>> <attachment_2.png><attachment_1.png>
>